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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ), 'gf_id' => 'HOM05D001324', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001324' ), 'data_identifier' => 'HOM05D001324', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001324', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '474', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p11330' => 'bna', 'A03p43260' => 'bna', 'A03p51810' => 'bna', 'A03p58290' => 'bna', 'A03p58300' => 'bna', 'A07p09030' => 'bna', 'A10p02500' => 'bna', 'Aa31LG1G20820' => 'aar', 'Aa31LG2G21800' => 'aar', 'Aa31LG6G1980' => 'aar', 'Aa31LG8G9910' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3444' => 'aag', 'Actinidia18171' => 'ach', 'Actinidia20822' => 'ach', 'Actinidia30142' => 'ach', 'Actinidia37532' => 'ach', 'Ah.11g048610' => 'amhyb', 'Ah.12g058400' => 'amhyb', 'Ah.13g072610' => 'amhyb', 'Ah.15g092790' => 'amhyb', 'AL1G13600' => 'aly', 'AL3G38070' => 'aly', 'AL7G23970' => 'aly', 'AL7G34780' => 'aly', 'Aqoxy2G03477' => 'aox', 'Aqoxy2G03701' => 'aox', 'Aqoxy2G03704' => 'aox', 'Aqoxy2G03705' => 'aox', 'Aqoxy6G02088' => 'aox', 'arahy.Tifrunner.gnm1.ann1.07S39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5HI5D0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8CV590' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ZK1J8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C4X96D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HX0053' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T6398M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6CSQK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YJKT09' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z1RXDB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZD9EP0' => 'arhy', 'AT1G03990' => 'ath', 'AT3G23410' => 'ath', 'AT4G19380' => 'ath', 'AT4G28570' => 'ath', 'ATR0568G137' => 'atr', 'ATR0736G148' => 'atr', 'Atru.chr4.2003' => 'acertr', 'Atru.chr5.1777' => 'acertr', 'Atru.chr8.2615' => 'acertr', 'Atru.chr8.2616' => 'acertr', 'AUR62002165' => 'cqu', 'AUR62002166' => 'cqu', 'AUR62008758' => 'cqu', 'AUR62010487' => 'cqu', 'AUR62015543' => 'cqu', 'AUR62025480' => 'cqu', 'AUR62030404' => 'cqu', 'AUR62030405' => 'cqu', 'BcaB03g14624' => 'bca', 'BcaC01g03373' => 'bca', 'BcaC05g24477' => 'bca', 'BcaC05g24478' => 'bca', 'BcaC06g32611' => 'bca', 'BcaC06g35519' => 'bca', 'BcaC09g51417' => 'bca', 'BcaNung01783' => 'bca', 'BcaNung03067' => 'bca', 'BcaNung03068' => 'bca', 'BolC1t01309H' => 'bol', 'BolC3t17581H' => 'bol', 'BolC5t29009H' => 'bol', 'BolC7t41895H' => 'bol', 'BolC7t45537H' => 'bol', 'BolC7t46111H' => 'bol', 'BolC7t46112H' => 'bol', 'BraA01t01077Z' => 'bra', 'BraA03t13466Z' => 'bra', 'BraA03t14272Z' => 'bra', 'BraA03t14892Z' => 'bra', 'BraA07t28697Z' => 'bra', 'BraA10t42518Z' => 'bra', 'C01p13340' => 'bna', 'C03p53160' => 'bna', 'C05p02310' => 'bna', 'C07p13990' => 'bna', 'C07p50360' => 'bna', 'C07p56320' => 'bna', 'C07p56330' => 'bna', 'CAN.G1078.7' => 'can', 'CAN.G1251.9' => 'can', 'CAN.G220.40' => 'can', 'CAN.G998.3' => 'can', 'CAN.G998.4' => 'can', 'CANSAT35G0952' => 'cansat', 'CANSAT78G1809' => 'cansat', 'CARHR003340' => 'chi', 'CARHR099380' => 'chi', 'CARHR226170' => 'chi', 'CARHR236360' => 'chi', 'Carub.0001s0315' => 'cru', 'Carub.0003s2367' => 'cru', 'Carub.0007s1210' => 'cru', 'Carub.0007s2185' => 'cru', 'Ca_08690_v3' => 'car', 'Ca_09848_v3' => 'car', 'Ca_18861_v3' => 'car', 'Ca_22459_v3' => 'car', 'Ca_25051_v3' => 'car', 'Cc01_g18050' => 'ccan', 'Cc03_g05800' => 'ccan', 'Cc08_g06040' => 'ccan', 'Cc11_g04070' => 'ccan', 'CDE04G1393' => 'cde', 'CDE08G0157' => 'cde', 'CDE08G0222' => 'cde', 'CDE11G0308' => 'cde', 'Cfa002456' => 'cfa', 'Cfa002458' => 'cfa', 'Cfa002459' => 'cfa', 'Cfa014744' => 'cfa', 'Cfa014745' => 'cfa', 'Cfa021066' => 'cfa', 'Ciclev10004403m.g' => 'ccl', 'Ciclev10004405m.g' => 'ccl', 'Ciclev10011111m.g' => 'ccl', 'Ciclev10018992m.g' => 'ccl', 'CiPaw.02G109200' => 'cil', 'CiPaw.03G267800' => 'cil', 'CiPaw.11G073900' => 'cil', 'CiPaw.12G055700' => 'cil', 'ClCG05G004190' => 'cla', 'ClCG07G001210' => 'cla', 'ClCG11G004020' => 'cla', 'ClCG11G016140' => 'cla', 'COL.COLO4_07001' => 'col', 'COL.COLO4_15918' => 'col', 'COL.COLO4_16744' => 'col', 'COL.COLO4_19544' => 'col', 'COL.COLO4_34372' => 'col', 'Cpa.g.c39162' => 'cpa', 'Cpa.g.sc165.33' => 'cpa', 'Cpa.g.sc2124.1' => 'cpa', 'Cpa.g.sc44.31' => 'cpa', 'CsaV3_3G011920' => 'csa', 'CsaV3_3G028130' => 'csa', 'CsaV3_4G014890' => 'csa', 'CsaV3_4G014900' => 'csa', 'CSS0014043' => 'camsi', 'CSS0025103' => 'camsi', 'CSS0027556' => 'camsi', 'CSS0032744' => 'camsi', 'CSS0035428' => 'camsi', 'CSS0036281' => 'camsi', 'DCAR_000925' => 'dca', 'DCAR_012565' => 'dca', 'DCAR_018502' => 'dca', 'DCAR_024279' => 'dca', 'DCAR_027330' => 'dca', 'Dinv13758' => 'din', 'Dinv16373' => 'din', 'Dinv27074' => 'din', 'Dinv29838' => 'din', 'Dinv37435' => 'din', 'Dinv37436' => 'din', 'Duzib138G0940' => 'dzi', 'Duzib151G0980' => 'dzi', 'Duzib205G0933' => 'dzi', 'Duzib212G0882' => 'dzi', 'ECA233G2798' => 'eca', 'ECA236G4142' => 'eca', 'ECA248G0785' => 'eca', 'ECA248G3225' => 'eca', 'EL10Ac3g04977' => 'bvu', 'EL10Ac5g12590' => 'bvu', 'EL10Ac5g12592' => 'bvu', 'EL10Ac7g17630' => 'bvu', 'EL10Ac7g17635' => 'bvu', 'EL10Ac7g17639' => 'bvu', 'Eucgr.D02566' => 'egr', 'Eucgr.D02568' => 'egr', 'Eucgr.H00753' => 'egr', 'Eucgr.H03017' => 'egr', 'Eucgr.K02114' => 'egr', 'FAN12G3682' => 'fan', 'FAN15G0508' => 'fan', 'FAN17G0317' => 'fan', 'FAN17G0886' => 'fan', 'FAN20G0642' => 'fan', 'FAN22G1374' => 'fan', 'FAN24G1405' => 'fan', 'FAN27G0459' => 'fan', 'FvH4_2g21000' => 'fve', 'FvH4_2g21040' => 'fve', 'FvH4_4g04030' => 'fve', 'Glyma.01G152900' => 'gma', 'Glyma.03G165200' => 'gma', 'Glyma.06G272200' => 'gma', 'Glyma.09G218100' => 'gma', 'Glyma.10G183000' => 'gma', 'Glyma.12G132800' => 'gma', 'Glyma.16G076300' => 'gma', 'Glyma.16G108900' => 'gma', 'Glyma.19G166500' => 'gma', 'Gohir.A07G150400' => 'ghi', 'Gohir.A09G228700' => 'ghi', 'Gohir.A10G109550' => 'ghi', 'Gohir.D07G156800' => 'ghi', 'Gohir.D09G229800' => 'ghi', 'Gohir.D10G157600' => 'ghi', 'Gorai.001G179800' => 'gra', 'Gorai.006G252500' => 'gra', 'Gorai.011G177100' => 'gra', 'GSVIVG01027855001' => 'vvi', 'GSVIVG01028371001' => 'vvi', 'GSVIVG01036891001' => 'vvi', 'HanXRQChr01g0015111' => 'han', 'HanXRQChr07g0202711' => 'han', 'HanXRQChr08g0227031' => 'han', 'HanXRQChr08g0227041' => 'han', 'HanXRQChr08g0227071' => 'han', 'HanXRQChr09g0264571' => 'han', 'HanXRQChr14g0434991' => 'han', 'Haze_08420' => 'cav', 'Haze_11420' => 'cav', 'Haze_11422' => 'cav', 'Hma1.2p1_0112F.1_g054310' => 'hma', 'Hma1.2p1_0262F.1_g105360' => 'hma', 'Hma1.2p1_0262F.1_g105370' => 'hma', 'Hma1.2p1_2140F.1_g314980' => 'hma', 'HPP92_002552' => 'vpl', 'HPP92_005128' => 'vpl', 'HPP92_008550' => 'vpl', 'HPP92_012691' => 'vpl', 'HPP92_012696' => 'vpl', 'Hund03056' => 'sun', 'Hund11909' => 'sun', 'Hund18260' => 'sun', 'Lalb_Chr01g0006041' => 'lal', 'Lalb_Chr01g0006051' => 'lal', 'Lalb_Chr01g0019591' => 'lal', 'Lalb_Chr02g0150301' => 'lal', 'Lalb_Chr03g0030061' => 'lal', 'Lalb_Chr05g0229251' => 'lal', 'Lalb_Chr05g0229271' => 'lal', 'Lalb_Chr16g0380451' => 'lal', 'Lj1C71G11' => 'lonja', 'Lj1g0008553' => 'lja', 'Lj2g0020750' => 'lja', 'Lj3g0018874' => 'lja', 'Lj4g0027468' => 'lja', 'Lj5g0005408' => 'lja', 'Lj6C627T4' => 'lonja', 'Lj8C362T1' => 'lonja', 'Lsat_1_v5_gn_2_39740' => 'lsa', 'Lsat_1_v5_gn_2_39781' => 'lsa', 'Lsat_1_v5_gn_2_39940' => 'lsa', 'Lsat_1_v5_gn_5_182601' => 'lsa', 'Lsat_1_v5_gn_6_17041' => 'lsa', 'Manes.03G162200' => 'mes', 'Manes.12G034700' => 'mes', 'Manes.15G043400' => 'mes', 'Manes.15G184700' => 'mes', 'Mapoly0065s0052' => 'mpo', 'MBI04_g06272_MAGBIO' => 'mbi', 'MBI07_g31082_MAGBIO' => 'mbi', 'MBI07_g32829_MAGBIO' => 'mbi', 'MBI07_g32830_MAGBIO' => 'mbi', 'MBI10_g13791_MAGBIO' => 'mbi', 'MD05G1193200' => 'mdo', 'MD10G1179700' => 'mdo', 'MD13G1216700' => 'mdo', 'MD16G1286200' => 'mdo', 'Medtr0651s0010' => 'mtr', 'Medtr1g075650' => 'mtr', 'Medtr4g080823' => 'mtr', 'Medtr4g080890' => 'mtr', 'Medtr5g025650' => 'mtr', 'Medtr7g097210' => 'mtr', 'Medtr8g072210' => 'mtr', 'MELO3C006405.2' => 'cme', 'MELO3C010528.2' => 'cme', 'MELO3C012854.2' => 'cme', 'Migut.A00473' => 'egut', 'Migut.D00452' => 'egut', 'Migut.D00453' => 'egut', 'Migut.E01379' => 'egut', 'Migut.G00501' => 'egut', 'MSTRG.11856' => 'ama', 'MSTRG.18337' => 'ama', 'MSTRG.4149' => 'ama', 'Nitab4.5_0000044g0590' => 'nta', 'Nitab4.5_0000236g0010' => 'nta', 'Nitab4.5_0000596g0030' => 'nta', 'Nitab4.5_0003295g0020' => 'nta', 'Nitab4.5_0006244g0010' => 'nta', 'Nn1g04503' => 'nnu', 'Nn1g09338' => 'nnu', 'Nn3g19722' => 'nnu', 'Oeu024802.1' => 'oeu', 'Oeu047807.1' => 'oeu', 'Oeu055791.1' => 'oeu', 'Oeu059408.1' => 'oeu', 'Oeu059414.1' => 'oeu', 'Oeu064642.2' => 'oeu', 'Os02g0621800' => 'osa', 'Os10g0474100' => 'osa', 'Os10g0474800' => 'osa', 'Os10g0474900' => 'osa', 'Os10g0475100' => 'osa', 'Peaxi162Scf00045g00821' => 'pax', 'Peaxi162Scf00045g01020' => 'pax', 'Peaxi162Scf00045g01023' => 'pax', 'Peaxi162Scf00045g01025' => 'pax', 'Peaxi162Scf00045g01026' => 'pax', 'Peaxi162Scf00199g00032' => 'pax', 'Peaxi162Scf00223g00094' => 'pax', 'Peaxi162Scf00415g00023' => 'pax', 'Peaxi162Scf00415g00215' => 'pax', 'Peaxi162Scf00415g00216' => 'pax', 'Peaxi162Scf00550g00440' => 'pax', 'Peaxi162Scf00602g00008' => 'pax', 'Peaxi162Scf00602g00112' => 'pax', 'PGR004G2775' => 'pgr', 'PGR031G0046' => 'pgr', 'PGR031G1408' => 'pgr', 'PGR031G3279' => 'pgr', 'PGR031G3556' => 'pgr', 'PGR083G0140' => 'pgr', 'PGSC0003DMG400001971' => 'stu', 'PGSC0003DMG400017211' => 'stu', 'PGSC0003DMG400018458' => 'stu', 'PGSC0003DMG400024294' => 'stu', 'Phvul.001G162800' => 'pvu', 'Phvul.002G122600' => 'pvu', 'Phvul.003G278200' => 'pvu', 'Phvul.010G070584' => 'pvu', 'Phvul.011G136600' => 'pvu', 'Potri.002G259700' => 'ptr', 'Potri.004G234900' => 'ptr', 'Potri.008G169300' => 'ptr', 'Potri.010G069100' => 'ptr', 'Pp3c10_7580' => 'ppa', 'Pp3c14_16140' => 'ppa', 'Pp3c2_4310' => 'ppa', 'Prupe.1G042400' => 'ppe', 'Prupe.5G013900' => 'ppe', 'Prupe.8G219700' => 'ppe', 'Psat0s2359g0040' => 'psa', 'Psat2g145000' => 'psa', 'Psat3g057160' => 'psa', 'Psat3g097880' => 'psa', 'Psat6g122520' => 'psa', 'Psat7g162840' => 'psa', 'PSO017G2391' => 'pso', 'PSO063G3508' => 'pso', 'PSO782G2154' => 'pso', 'PSO832G1769' => 'pso', 'QL06p019705' => 'qlo', 'QL09p040216' => 'qlo', 'QL09p040231' => 'qlo', 'QL12p003534' => 'qlo', 'QL12p003548' => 'qlo', 'RcHm_v2.0_Chr4g0394301' => 'rch', 'RcHm_v2.0_Chr6g0287381' => 'rch', 'RcHm_v2.0_Chr7g0215241' => 'rch', 'Rhsim01G0090900' => 'rsi', 'Rhsim01G0091000' => 'rsi', 'Rhsim04G0176000' => 'rsi', 'Rhsim07G0140600' => 'rsi', 'Rhsim13G0037900' => 'rsi', 'Sabra01G0179600' => 'sbr', 'Sabra02G0197600' => 'sbr', 'Sabra03G0042300' => 'sbr', 'Sabra03G0042400' => 'sbr', 'Sabra08G0129200' => 'sbr', 'Sabra10G0038000' => 'sbr', 'SalBow4G0615' => 'sbo', 'SalBow4G2259' => 'sbo', 'SalBow8G0470' => 'sbo', 'SalBow8G5026' => 'sbo', 'Sc07g0008050' => 'sci', 'Sc07g0008060' => 'sci', 'Sc24g0003700' => 'sci', 'Sc25g0003650' => 'sci', 'Sed0000449' => 'sed', 'Sed0012772' => 'sed', 'Sed0013034' => 'sed', 'SEGI_04388' => 'sgi', 'SEGI_24258' => 'sgi', 'SEGI_27403' => 'sgi', 'SEGI_27492' => 'sgi', 'SEGI_33190' => 'sgi', 'SEGI_38972' => 'sgi', 'SEGI_41396' => 'sgi', 'SGA_v2.0_scaffold138G35203' => 'sas', 'SGA_v2.0_scaffold144G35890' => 'sas', 'SHI32763' => 'shi', 'SHI32764' => 'shi', 'SMO196G0016' => 'smo', 'SMO234G0068' => 'smo', 'SMO367G0257' => 'smo', 'SMO367G0513' => 'smo', 'Solyc08g005630.3' => 'sly', 'Solyc08g075240.3' => 'sly', 'Solyc08g075250.1' => 'sly', 'Solyc08g075260.1' => 'sly', 'Solyc08g075270.1' => 'sly', 'Solyc09g072610.3' => 'sly', 'Solyc09g090350.3' => 'sly', 'Sopen08g001680' => 'spe', 'Sopen08g023840' => 'spe', 'Sopen08g023850' => 'spe', 'Sopen08g023870' => 'spe', 'Sopen09g028420' => 'spe', 'Sopen09g033250' => 'spe', 'Sp1g02830' => 'spa', 'Sp3g21080' => 'spa', 'Sp7g17990' => 'spa', 'Sp7g26560' => 'spa', 'TAR365G0558' => 'tar', 'TAR625G0210' => 'tar', 'TAR625G0729' => 'tar', 'TAR636G0860' => 'tar', 'TAR636G1690' => 'tar', 'TAR636G1930' => 'tar', 'TAR636G3416' => 'tar', 'TAR636G3541' => 'tar', 'THA.LOC104804041' => 'tha', 'THA.LOC104806100' => 'tha', 'THA.LOC104808642' => 'tha', 'THA.LOC104808643' => 'tha', 'THA.LOC104808644' => 'tha', 'THA.LOC104808645' => 'tha', 'THA.LOC104812891' => 'tha', 'THA.LOC104820072' => 'tha', 'Thecc.01G254000' => 'tca', 'Thecc.03G320700' => 'tca', 'Thecc.04G259200' => 'tca', 'Thhalv10006882m.g' => 'esa', 'Thhalv10020141m.g' => 'esa', 'Thhalv10024496m.g' => 'esa', 'Thhalv10024528m.g' => 'esa', 'TPR.G10078' => 'tpr', 'TPR.G10890' => 'tpr', 'TPR.G13808' => 'tpr', 'TPR.G16215' => 'tpr', 'TPR.G17315' => 'tpr', 'TPR.G29572' => 'tpr', 'TPR.G29573' => 'tpr', 'TPR.G29637' => 'tpr', 'TPR.G32104' => 'tpr', 'TPR.G39527' => 'tpr', 'TPR.G40705' => 'tpr', 'TPR.G8983' => 'tpr', 'TPR.G9201' => 'tpr', 'TWI09G0066' => 'twi', 'TWI12G0220' => 'twi', 'TWI18G0879' => 'twi', 'TWI34G1888' => 'twi', 'vmacro02693' => 'vma', 'vmacro08513' => 'vma', 'vmacro13861' => 'vma', 'vmacro19832' => 'vma', 'vmacro23442' => 'vma', 'VMungo0251G3610' => 'vmu', 'VMungo0720G1462' => 'vmu', 'VMungo1127G0502' => 'vmu', 'VMungo1127G0772' => 'vmu', 'VMungo1215G2629' => 'vmu', 'VMungo1309G2660' => 'vmu', 'VMungo1383G1084' => 'vmu', 'Zm00001eb045960' => 'zma', 'Zm00001eb045990' => 'zma', 'Zm00001eb185040' => 'zma' ) $gf_id = 'HOM05D001324' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001324' ) $data_identifier = 'HOM05D001324' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 6, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 4, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 6, 'egr' => (int) 5, 'fan' => (int) 8, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 4, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 5, 'pax' => (int) 13, 'pgr' => (int) 6, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 3, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 2, 'shi' => (int) 2, 'smo' => (int) 4, 'sly' => (int) 7, 'spe' => (int) 6, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 8, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 13, 'twi' => (int) 4, 'vma' => (int) 5, 'vmu' => (int) 7, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb185040' $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